On Thu, Jul 21, 2011, Wei Chen wrote:
>
> After I solvated my protein, I used "addIons" to add ions to the
> system to reach certain ion concentration. I found that some ions were
> placed outside of the water box. Is this normal? When I used AMBER8
> long time ago, this did not happen. I was wondering if this is
> something with the new version of AmberTools.
It's been seen before I think: http://archive.ambermd.org/201007/0205.html
(Just use the search box on the Amber mailing list web page). But I don't
know that it was ever resolved, so if Dan is willing to look at it, that is
fine. Presumably, (a) most people never study the distribution of ions too
closely, and/or (b) equilibration makes the simulation forget about the
details of the intial condition anyway.
....dac
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Received on Fri Jul 22 2011 - 05:30:03 PDT
